An in vivo study was carried out on uncoated and hydroxyapatite (HA)-coated nanostructured Ti13Nb11Zr alloy in comparison with high-grade Ti6Al4V, to investigate the effect of the different surfaces on osteointegration rate. A highly effective method to obtain a fast biomimetic deposition of a thin layer of nanocrystalline HA was applied to coat both substrates. Cylindrical pins were implanted in rabbit cortical bone and evaluated at 4 and 12 weeks by histomorphometry and microhardness tests. The results confirmed the ability of the slightly supersaturated Ca/P solution to induce a fast deposition of nanocrystalline HA on Ti alloys' surfaces. HA-coated Ti13Nb11Zr had the highest osteointegration rate at 4 and 12 weeks. Both HA-coated surfaces showed an affinity index significantly higher than those of native surfaces at 4 weeks (Ti13Nb11Zr+HA: 37%; Ti6Al4V+HA: 26%). Microhardness test showed a significantly higher bone mineralization index of HA-coated Ti13Nb11Zr in comparison with that of HA-coated Ti6Al4V surface. The study suggests that the HA coating on both alloys enhances bone response around implants and that there is a synergic effect of Ti-Nb-Zr alloy with the HA coating on bone remodeling and maturation.